My understanding of it is the following: If there are two or more multi-domain proteins of similar structure/function, etc., and if they have a different orientation of a particular domain, then when you superimpose the two structures, they will not superimpose completely because of the domain that is juxtaposed differently in the two proteins with respect to the rest of the protein. The 'angle between domains' would then be the angle through which that domain2 must be rotated to align it with domain1.
This angle would not result in a complete definition of the geometrical transformation required to superimpose the two domains, but it will give a kind of physical/tangible idea of the the relative domain swing between the two proteins. For example, if the Reverse Transcriptases from mouse and human are superimposed (overall similar protein size, 5 domains: Fingers, Palm, Thumb, Connection and RnaseH), the fingers and palm domains align quite nicely, but there is a swing angle of approx. 70 degrees or so, between the connection domains from the two proteins. Thanks, Debanu. -----Original Message----- From: Bernhard Rupp [mailto:[EMAIL PROTECTED] Sent: Sat 7/7/2007 8:21 PM To: Das, Debanu; CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] how to convert matrix to angle Not that I want to open a can of worms here... but could someone explain what is meant with 'angle between domains'? Thx, br -----Original Message----- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Das, Debanu Sent: Saturday, July 07, 2007 7:51 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] how to convert matrix to angle Hi, You can also use LSQKAB in CCP4 to get the angle between two similar domains. -Debanu. -----Original Message----- From: CCP4 bulletin board on behalf of Kay Diederichs Sent: Sat 7/7/2007 7:30 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] how to convert matrix to angle Jiamu Du schrieb: > Dear all: > I want to calculate the rotation angle between two similar domains. By > using Coot, I can superposr the two domain and get the rotation matrix. > But how to convert this matrix to an angle. Is there any program can > calculate this ? > Thanks. > Jiamu Du, If you have the rotation matrix a11 a12 a13 a21 a22 a23 a31 a32 a33 then (a11 + a22 + a33 - 1) / 2 is the cosine of the angle you're looking for. HTH, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
